Shinji: Path of the Shinobi
by animefan29
Summary: Eva/Naruto crossover. When Gendo abandoned Shinji to be taken care of by a teacher, he did not expect the boy to be taken by another to a land unaffected by Second Impact. Shinji, trained by Jiraiya and Konoha will be a force to be feared. rated T for now
1. Chapter 1

**Shinji: Path of the Shinobi**

**Disclaimer: **I do not own Evangelion or Naruto

"Hello" – Speaking

'_Hello_' – Thoughts

"**Hello**" – **Demon/Boss Summon Speaking/Techniques**

'_**Hello**_' – **Demon/Boss Summon Thoughts/Techniques**

* * *

A small four year old child sat crying on a bench in a train station. This brown haired, blue eyed child is Shinji Ikari. It is the year 2005 and he has just lost his mother who was absorbed into the robot she was working on called Evangelion, but that memory was already starting to fade from the young boy's mind. Now a few days later he had been abandoned by his father who said that he no longer had a use for the boy.

The boy's father, Gendo Ikari, had said that Shinji would be picked up at the train station by his new care taker and had departed, completely ignoring the small child's cries for him to not go. Gendo had even ignored the tall, white haired, man with the antiquated clothes, red markings on his face, and a metal headband that had the kanji for oil on it. Jiraiya of the Three Legendary Sannin had witnessed the entire abandonment from start to finish.

Jiraiya was on an assignment to gather information on the world outside of the Hidden Continent that was the home to the shinobi world. He had just finished setting up his own personal spy network back in the Elemental Countries when the newly appointed Yondaime Hokage had requested that he work to update the one Konohagakure had for the outside world.

Jiraiya's mission hadn't started a moment too soon. Shortly before he left the Land of Fire there was a huge cataclysmic event called Second Impact. The following aftermath of death and destruction had left the spy networks of all the Hidden Villages in shambles, and with the recent war they had little manpower to try and repair them. So Jiraiya had spent the last four years wandering the world gathering informants, allies, and establishing methods to keep them in contact. He felt lucky that most information concerning the outside world was worth little in the Elemental Countries and he wouldn't have to handle it himself, with most of the handling of information from this network being done by a Chuunin squad.

Now Jiraiya had mostly finished with only Japan left to establish contacts in, and he still had a few months before he head to report back in. By sheer chance he had ended up at the same train station where Shinji had been abandoned and he had seen the whole thing. Now Jiraiya is many things, a legendary shinobi, a writer, a pervert (or as he says a SUPER-PERVERT), but what most people don't know is that he is a real softie for children. This softness is what led him to train three orphans in the war-torn Land of Rain. And it was this same softness the directed him to the crying child sitting on a bench waiting for some stranger to pick him up.

Being a master ninja it wasn't hard for Jiraiya to walk up and start talking to the little boy. He quickly gained the child's trust and soon knew the kid's entire life story. At first it was the same life that all children should have; all sunshine and giggles. But with the 'death' of his mother and the loss of his father Shinji had started to develop psychological scars that would hamper him later in life. On the bright side, the scars were still fresh and could be healed. As long as they weren't left to fester Shinji would become more or less a normal boy. Jiraiya felt that he could help heal the boy, the same way he helped Yahiko, Nagato, and Konan. Train him into a ninja.

Shinji had readily agreed to the training, although that might have been because he was under the impression that this was the man who was supposed to take care of him. But he's four, it's an understandable mistake. Now all Jiraiya had to do was put the guy Gendo assigned to watch Shinji under a good Genjutsu and they would be good to go.

* * *

(Time Skip – 4 months)

Jiraiya sat on a log in a forest clearing where he observed his latest student go through several exercises that would help improve his ability to throw shuriken.

It had been four months since he had picked up the small boy, and he felt those months well spent. Shinji had proved early on that he had a real knack for picking up skills and understanding the basic principle about how things were done and why.

At first the boy was incredibly shy and withdrawn from the world, but with the Sannin's help he had started to overcome that. He was now a lot more outgoing and responded better to new things. It had helped that he became eager to learn 'cool ninja tricks' after Jiraiya had shown him the basics such as the Henge, or when he cut a fly in half with a shuriken.

Shinji had quickly grasp what chakra was, even if he was a little young to understand how to control it, but Jiraiya figured that he would be doing the tree climbing exorcise long before most Genin do it. He was also developing nicely physically with the daily exercises his teacher had him doing.

Heck, Jiraiya would have been glad that he decided to bring Shinji along even if the boy wasn't turning out to be a student to be proud of. And that was because Shinji was helping Jiraiya with his research, even if the kid didn't know it. Anytime the two came to a hot springs, Jiraiya would somehow manage to trick Shinji into wandering into the women's side of the springs. The women would then swoop on Shinji and start proclaiming how cute and adorable while pinching his cheeks and musing his hair. Then Jiraiya would call through the door asking if his 'nephew' was in there. This was usually good for several minutes of free ogling of pretty women clad only in towels, sometimes not even that much. Shinji eventually wised up and stopped falling for the older man's tricks, but by then Jiraiya had already written one book and was working on the manuscript of another. But that's in the past and isn't important, well Kakashi would think it's important but he doesn't know about it.

"Hey Shinji! You can stop now, we have something important to discuss!" Jiraiya called to his student.

"What is it Jiraiya-sensei?" Asked Shinji as he stopped his exercises. The boy had figured out that Jiraiya was not the man Gendo had said would watch him, but he was happy now and didn't care.

"Listen, as you know I'm setting up a spy network. What you don't know is that I am about finished. When I am, I will have to go back to my home village in the Land of Fire. Remember what I said about the Hidden Continent and the world there?"

Shinji nodded, wondering what would happen to him once it was time for Jiraiya to leave.

"Well when I leave, you will be presented with two options that will change your life. First, you can stay here in Japan. I can have you taken to the teacher your father wanted you to be with. If you choose that then your training under me will be finished and you will never see me or anyone else from the Elemental Countries ever again." Shinji's did not like the sound of that option as it sounded exactly like what Gendo had done to him. "Or, you could come with me back to Konoha. There you can continue your training and become a shinobi, or you could try some other profession. I won't have the time to watch over you like I do now, but I will be able to drop by from time to time and give you a bit of personal training. What do you say?"

Shinji didn't even think about it for a second. "I want to go with you and become a shinobi."

Jiraiya grinned at the conviction in the boy's voice. "You know, I kind of had a feeling that would be the option you chose."

* * *

Jiraiya and Shinji casually strolled down a path in the forests of the Land of Fire. It couldn't be seen through the trees but they were drawing close to Konohagakure, the Village Hidden in the Leaves.

Shinji had to admit that this Hidden Continent was very different from Japan. For one thing, ever since they got off the boat they had walked everywhere, with not a single car or train. When he asked Jiraiya about this the Toad Sannin had replied that many of the technological conveniences of the outside world were considered either useless or more harmful than helpful, such as the internal combustion engine. Sure it could be used in a car to get a person from point A to point B quickly and smoothly, but there was no real need for it. Ninja with their stamina and speed were considered more efficient and cheaper then paving over the country side with roads then spending money to either buy or build the vehicles, not to mention the known pollution that came with them. And where would they get the oil from and still remain hidden?

That didn't mean that all modern conveniences were frowned upon. Electric lights and cooking appliances, indoor plumbing, and modern medical equipment and medicine were all received with open arms, although the medical equipment and medicine was sometimes found to be inferior to medical jutsus and shinobi medicine, but they were handy in places without ninja. They were even constantly importing and reprinting various forms of literature whether it is a science journal to manga to one of the classics by Shakespeare, although Jiraiya liked to brag that his books were a lot more popular then the playwright's.

Now this led to one question that Shinji had been wondering for some time. How did the Hidden Continent stay hidden? Jiraiya had said that that was one of the biggest mysteries in the world. No one knew why, but there was a barrier that covered a large portion of the Pacific Ocean. Within that barrier was every single one of the Elemental Countries from the northern Land of Snow, to the southern Sea Country. Some people theorized that it was the Rikudou Sennin, creator of Ninjutsu that erected the barrier. Other's thought it might have been the Bijuu who did it, or at least people who wanted to keep the Bijuu contained. The only thing that they did know was that barrier seemed to repel ordinary people, and the only way to get in was to be guided by someone who could manipulate their chakra as they were the only ones whom the barrier did not affect.

This left Shinji with a lot of information to think over as he and his teacher walked towards his new home. He found that over all their reasons for not having cars made sense as the only people who did a lot of traveling around here were generally ninja on a mission, and even though his training hadn't been going on for very long yet Shinji was not tired despite the days he had spent walking practically nonstop.

Eventually teacher and student made it to the tall large gates that were the entrance to the Hidden Village. And Shinji got to see some ninja besides Jiraiya for the first time.

"Hold it you two; we're going to need some ID before we can let you into the village." Said one of the two Chuunin that had gate guarding duty.

Jiraiya puffed himself up and started laughing boisterously. "HA HA!! ID!? Don't you know who I am!? I am the Great Sage of Mt. Myobokugama, known North, South, East, and West as the Legendary Toad Sannin Jiraiya!" This exclamation was accompanied by a short dance that involved a lot hopping around on one foot and finally summoning a horse sized toad at the end.

Shinji and the Chuunin sweatdropped at the sight. Shinji couldn't believe how ridiculous his teacher's introduction was, and the Chuunin couldn't believe that this was one of their strongest shinobi. But the ability to summon toads only belonged to one ninja, so that was proof enough.

"Ok…" said one of the Chuunin. "You're definitely Jiraiya-sama…_Although I don't know if that's a good thing_…but who's this child with you?"

"This is Shinji Ikari, a student I picked up on my travels. When I report to the Hokage I am going to see what I can do about getting him a place to live before enrolling him at the academy." Said Jiraiya as he presented his ward.

"Alright then, you two can go on in." Said the other Chuunin. "You should head straight to the Hokage Tower, we were told to expect you any day now and send you right there once you got back from your mission."

"Ahhh, damn gaki. He knows that I like relaxing at the hot springs as the first thing I do when I get back into town." Grumbled the white haired Sannin as he and his brown haired student made their way into the village.

The Chuunin looked at each other before the younger of the two said, "Doesn't he know about what happened three years ago?"

Shaking his head the elder said, "No, he left for a long term mission to the outside world shortly before it happened. There hasn't been a word of communication that's reached him since he left."

"Then shouldn't we have warned him? I mean he was the man's teacher."

"Nah, he should be told by someone who is close to him. Probably a good thing he's taken that kid under his wing though."

* * *

"Hey Jiraiya-sensei, what's the Hokage?" Asked Shinji as he and the perverted Sannin made their way through the village of Konoha.

"The Hokage is the leader of Konoha and is considered its strongest ninja." Explained Jiraiya. "If you look up there you will see the carved faces of the four Hokages that Konoha has had." He said as he pointed to the mountain at the back of the village that had four faces carved upon it. "The one at the left is the Shodaime Hokage a member of the Senju clan and who founded the village about 70 years ago. Then there is the Nidaime Hokage, who was the Shodaime's younger brother. Next to him is the Sandaime Hokage, Sarutobi-sensei as I call him since he taught me and the other two Sannin everything we know. And finally the spiky haired urchin at the right is the Yondaime Hokage, Minato Namikaze and my student. He's the guy who sent me out to set up a spy network in the outside world and he's the guy we're going to meet."

The two soon reached the tower and walked quickly and quietly through the lower levels, making their way to the Hokage's office at the top. The secretary outside the office didn't even try to stop them as she recognized the Toad Sannin.

Jiraiya, who usually preferred to come in through the window while sneaking up on the Hokage, decided that if you can't use Plan A go with Plan B. Kicking open the door he shouted, "HEY GAKI! DON'T YOU KNOW IT'S RUDE TO CALL A NINJA WHO'S BEEN ON A LONG, TIRING MISSION STRAIGHT TO YOUR OFFICE WHEN HE GETS BACK! I SHOULD GET A CHANCE TO RELAST AT THE HOT SPRINGS FRIST! IT'S BEEN SO LOng since I could enjoy the view…?" Jiraiya had trailed off in confusion at the sight of not his student the Yondaime but his teacher the Sandaime sitting behind the desk wearing the robes he gave up when he retired. "Sensei? What are you doing here? Where's Minato?" He asked.

"It's good to see that you've returned Jiraiya." He said while motioning to the empty seats in front of his desk. "Please seat down, there is much that needs to be discussed."

Jiraiya moved forward and sat down while Followed by Shinji who had been behind his teacher and had yet to be noticed by the Sandaime.

"Oh? And who is this young lad that you've brought with you?" Queried the Sandaime.

"This is a student I picked up while I was in Japan. His name is Shinji Ikari. Shinji say hello to my sensei the Sandaime Hokage."

"Hello"

"I'll explain later sensei. Now what is it you wanted to talk to me about?"

In the village of Konoha all activity ceased as a loud "WHAAAAT!?" could be heard from the Hokage Tower.

The news was such a surprise to Jiraiya that he practically had a heart attack. The Kyuubi had attacked Konoha almost a year after he left. In an attempt to stop the Kyuubi, Minato used a forbidden sealing technique that cost him his life. But if Minato was dead, then what about his wife or unborn child. Actually he had a funny suspicion about baby. "Sensei, what happened to Kushina and their baby?" He asked nervously.

Sighing Sarutobi said, "I'm sorry to say that one the same night Kushina died due to birth complications. As for their child, well there is someone I want you to meet." Pressing the intercom button on his desk he asked his secretary to have Iruka brought in.

Within a minute a young sixteen year old Chuunin walked into the office followed by a three year old boy wearing a white T-shirt with tan shorts and blue sandles. The child has spiky golden-yellow hair, cerulean blue eyes, and three whisker marks on each cheek. Shinji felt as if he had seen that face somewhere before but couldn't quite remember where.

"Jiraiya, this is Naruto Uzumaki. His birthday is October 10th." Introduced the Sandaime.

That was all Jiraiya needed to know who the kid was and what he was. "Shinji," he said, "why don't you go with Naruto here and play with him? You'll keep an eye on him…Iruka wasn't it?" He asked the Chuunin who answered in the affirmative. "Good now you three run along while I talk to sensei."

When the three had left the room Jiraiya turned to the Hokage and said, "We need to talk."

After several hours of discussion the two had gotten their stories told. Sarutobi told his student about the Kyuubi's attack and what Minato did to stop it. Then he talked about all the steps he had taken to protect Naruto from the dangers of being Minato Namikaze's son, and from the prejudice that usually came with being a Jinchuuriki. Unfortunately he wasn't quite as successful with the latter. Sure no one Naruto's age knew the truth and those who were too young at the time to understand didn't really know it either, but the fear and hate of their parents had rubbed off on the children and it leaves an impression on a child when a parent forces them away from someone while saying they were dangerous. Luckily there were those among the people like Iruka who were willing to look past the fact that Naruto contained a demon and got to know the true child that he was. Jiraiya in turn told Sarutobi everything that had happened while he was setting up his spy network. He highlighted most of it until the point he met Shinji. He talked of how he was in a train station when he saw a bearded man tell Shinji that he was no longer needed and was sending him away to live with some stranger. Jiraiya then mentioned how he talked to the boy and found out everything that there to the boy. Sarutobi had approved of how Jiraiya decided to help the boy and promised to arrange everything for Shinji to live in Konoha. But he was more interested in the organization GEHIRN. Jiraiya said that he managed to get a few informants in the place, but they were mostly low-level techs and other similar low-profile characters that would only be able to provide a little more information besides what was publicly known. The only real piece of interesting information that he had was the E-project GEHIRN was working on.

"Well, if that is all the information that you have Jiraiya then I will select a team of shinobi to handle your contacts there. For now I need you working here in the Elemental Countries." Said Sarutobi.

"Alright sensei, but what do you plan to do about Shinji's living arrangements? It's not like you can just put a small child in an apartment on his own."

"No your right. For a while now I had been planning to have Naruto live with Iruka. I feel that it will do Shinji good to live with them." Replied the Sandaime as he started filling out the appropriate forms. "Of course you do know that you are technically their guardian?"

"HUH? How did that happen?" Asked Jiraiya.

"Well, since Shinji is technically an orphan and you took him in as a student that makes him your responsibility. And Minato had decided to name you Naruto's godfather. As such you are their legal guardian. However we have a pressing need for you and your information gathering techniques, so they will be in Iruka's custody whenever you are not in the village."

"Man this is going to put a cramp in my style." Whined Jiraiya.

"Oh? You never complained when you had a Genin team. How is this different?"

"Because I was just a sensei to them. To these kids I will practically be their parent. It will be my job to give them a path to follow in life."

"Trust me, I'll make sure they follow Iruka's example before they follow yours." Said the Sandaime.

"Thanks for the vote of confidence sensei."

"Listen, it is getting late and I think it's time we got Iruka, Naruto, and Shinji to their new home."

By the end of the day they had all of Shinji's and Naruto's stuff in Iruka's apartment. Jiraiya stayed for a few days after that getting to know Iruka and Naruto while setting up a training schedule for Shinji and Naruto to follow until he got back. When it was time for Jiraiya to leave there were a few tears shed by Shinji but he brightened up when Jiraiya promised that they would see each other again in just a few months.

* * *

(Time Skip – two years)

Shinji was now six years old and would be joining the academy today. This was a day he had waited years for.

Over those years he had grown rather close to both Naruto and Iruka whom he saw as a little brother and an older brother respectively. Because Iruka was a Chuunin he was called away on a lot of missions, but that was alright since he always got someone to watch over his two little brothers. They were generally Chuunin like himself and were often very friendly to the boys. Although Shinji had felt that Anko was a little too friendly, bordering on amorous with Iruka. And did she have to keep throwing dango sticks into the wall trying to make a design?

He almost felt sorry for Naruto who was being watched by her right now. The key word being almost. He knew that neither would do anything to hurt the other and he was more excited about meeting the students and making some friends.

Entering the classroom he immediately spotted several students that made it there before him. One was a black haired boy with bushy eyebrows. The other was a girl wearing what he recognized as pink Chinese style clothes who was twirling a kunai around her finger from the handle ring.

It wasn't long after that the room filled up with other students and Shinji's eyes moved over to a boy with white blank eyes. He had seen others with those kinds of eyes and asked Iruka about it who said that they were members of the Hyuuga clan who were famous for their Doujutsu the Byakugan. After hearing about the Byakugan and its rival the Sharingan Shinji thought it would be pretty cool to have a Doujutsu.

Soon the class's Chuunin instructor walked in followed by someone very familiar to Shinji. "Hello everyone. I am your teacher Ryoga Hibiki and this is my assistant Iruka Umino. Today you will be starting your training as ninja, but I warn you now. Being a ninja is not a game. You will be called upon to complete missions that will require you to take another human life, or have your life taken instead. You will be asked to infiltrate fortified enemy positions in order to retrieve valuable information. Many ninja are killed before they are twenty, and from there it only gets more dangerous. So I ask anyone who doesn't think they can handle it to leave now."

Ryoga looked over the students and saw that some shook with apprehension, others shone with excitement, and some acted as if they were completely uninterested. But not one got up to leave, and he smiled at that letting his fang like canines show. "Very good you all just passed your first lesson. Always remember that battles between shinobi are more often mental rather than physical. If you allow yourself to be intimidated then you've already lost half the battle. So I congratulate you for not backing down, but remember that out in the real world you will face much tougher and more intimidating situations then this." The feral grin was soon replaced by a jolly smile as his attitude did a 180. "Now take out your texts and open to page five. We will now be studying shinobi history."

* * *

(Time Skip – four years)

Shinji loved his time spent at the Konoha academy. In the four years he had been attending he had developed several close friends. His best friend was Rock Lee (this is the only name I am putting in Japanese format of surname first and given name last, because it sounds a lot better than Lee Rock). Sure Lee wasn't that good in most of the classes, and for some reason he was unable to perform Ninjutsu or Genjutsu but that did not deter him from his dream of being an excellent Ninja. So to compensate he practiced his Taijutsu and he quickly rose through the ranks until the only two that good beat him were Shinji and Neji Hyuuga. Of course this didn't help his other grades and he was currently the dead last of the class.

Neji was more or less a pseudo friend of Shinji's. It might be more accurate to say that the two were rivals for the top spot in the class, which Shinji had held ever since the first day. It irritated Neji to no end that Shinji who came from no clan much less one as strong as the Hyuuga easily beat him an every subject they tested in. The only skill Neji came close to matching Shinji in was Taijutsu and he would often say that the only reason Shinji won was because he wasn't allowed to use Juuken (Gentle Fist) considering how damaging it was.

Another friend Shinji was close to was Tenten Higurashi. She was one of the top kunoichi of the class and was one of the best in projectile weapons, again second only to Shinji.

Shinji heard a lot of people muttering how he was a prodigy, but he laughed it off saying that his skills were due to the fact that he had been trained by Jiraiya of the Sannin ever since he was four. But still people kept saying that he was the best since Itachi.

Shinji was currently headed towards the principal's office. It had been decided that because of the skills Shinji had shown he would be given the Gennin exam early. When he got to the principal's office he was given a paper test that he quickly answered with 100 percent accuracy. Next was the weapons test which was observed by Iruka who had become a full teacher since Shinji's first year. After nailing all the targets right in their center he was taken to a Taijutsu field where he fought the assistant instructor Mizuki. Shinji had been underestimated because of his age and he accidently brook Mizuki's nose when he punched the teacher in the face. Finally Shinji was tested in Ninjutsu where he pulled off all three of the academy jutsu perfectly. And for extra credit he even performed the Katon: Endan technique that Jiraiya taught him.

Now he was back in principle Hibiki's office where his first teacher presented him with a brand new Konoha Hitat-ate. "Now Shinji you will have to come back Monday morning after you get registered so that you can be assigned to your Genin team." He told the happy boy who nodded in understanding before dashing off to show Naruto that he was an official shinobi now.

* * *

(Time Skip – four years)

Shinji snuck into the lair of his foe. He was a Chuunin now and was on an incredibly dangerous mission. One wrong move and everything would be ruined and the mission a failure. He silently closed in on his sleeping target, weapon poised in his hand. If the sleeping figure awoke then he was as good as dead. He looked on the face of his target who looked quite peaceful and almost angelic in his sleep. But Shinji knew better. Behind that innocent face was a sadistic monster that would make his life a living hell. He wouldn't be killed, oh no that is too easy for the beast. Instead it would torture Shinji into insanity, just has it had been for many years now. But now was the moment of where Shinji would get his revenge and it was going to be sweet. Shinji lowered his hand and let his weapon of choice fall onto his target.

The water splashed Naruto's face and the thirteen year old boy sat straight up spluttering. "Aniki!" He shouted as he started to shiver. Shinji had used ice water to make it more effective.

"Sorry bro, consider this the revenge I spoke of when you turned my hair blue last week." Said Shinji who had a great big grin of satisfaction on his face.

"I only did that because you put Jalapeño peppers into my ramen! You do not put Jalapeño peppers into ramen!" Naruto shouted at his older brother as he got out of bed to get some dry clothes before heading to the bathroom.

"And that was retaliation for putting hot sauce on my dango. You should feel fortunate that I didn't tell Anko what you did. She is as protective of dango as you are of ramen, and she is a lot more sadistic then I am. Remember what happened the time Jiraiya-sensei peeked on her while she was bathing?" He asked.

"Hey Ero-sennin had that coming to him." Retorted Naruto from behind the bathroom door. "You think that he would learn his lesson one of these days, but noooo. He has to keep peeking at naked or scantily clad women."

"Says the boy who invented the Oiroke no Jutsu." Shinji mutters as he made his way to the kitchen to finish cooking breakfast.

These was a fairly common occurrence in the Ikari-Umino-Uzumaki residence. Naruto liked to sleep past the time his alarm clock was set to and Shinji liked waking him up when he over slept. Eventually it had become common part of the prank war that Shinji and Naruto had. This war eventually came to include the whole village with the only people who were truly safe from pranks being the Sandaime, Iruka, and Anko. The first two out of respect, the third out of fear. Everyone else was fair game in their minds. Well Shinji tried to rein it back before it got out of hand but their motto was, "Just because we haven't pranked you, doesn't mean we won't."

After waking Naruto, Shinji would then go and finish breakfast preparations. It was usually just the two of them for breakfast as Iruka was very busy at the academy, so the task to make breakfast fell to Shinji. If he didn't fix the meals all he could expect to eat was ramen.

Soon Naruto was out of the bathroom wearing orange clothes with green goggles. Naruto had taken to training under Jiraiya whenever the Sannin was in town, and the effects of the training clearly showed. Sure he wasn't the top student, actually he was pretty close to the bottom, but that was because he was very good at academics which made up a third of their total grade. The other problem was that he sucked at Genjutsu and his weapons skills were pretty mediocre. His saving grace was that he was pretty good at Taijutsu and Ninjutsu, except for the Bunshin but Jiraiya tested the amount of chakra he had taught him Kage Bunshin to compensate. Shinji also learned Kage Bunshin as he had a lot of chakra for a guy his age, but he didn't have nearly the amount Naruto had and was forced to use it more strategically.

After a breakfast of miso soup and rice (much to Naruto's chagrin as he wanted ramen) Shinji started cleaning up as Naruto prepared for another day at the academy.

"Hey Aniki." Naruto called. "Didn't you say that you would be receiving a pretty important mission today?"

"Yeah I did Naruto. Hokage Ojisan had said that this was a B-ranked mission that he had been keeping reserved for me. Said that I would do better at it then most Jounin."

"Ah that is so cool. I wish I could go on important missions like that."

"Well this is your last year of the academy. Then you have to become a Genin and go on D-ranked missions. You won't get any real missions until you're a Chuunin and if your Jounin sensei is anything like me that will take a few more years." Indeed Shinji's sensei, Aoba Yamashiro, had trained his team for two years doing over 200 D-ranked missions and 20 C-ranked missions before he had deemed them ready for the Chuunin Exam. At the age of twelve Shinji was promoted to Chuunin after which he traveled and trained with Jiraiya learning the ins 

and outs of information gathering, only stopping by the village roughly every three months. Now at fourteen Shinji was already considered an elite Chuunin of the village who could get promoted to Jounin at anytime he wanted. When asked why he didn't want to Shinji said that he wanted to wait until Naruto became a Genin and when he had gotten the hang of elemental manipulation. "That is if you can graduate from the academy first." Shinji teased as he put on his Chuunin vest, knowing the kind of reaction that got from his brother.

"Hey I'll show you! I'll ace my exam and then impress my sensei so much with my awesome skills that he'll let me take the Chuunin Exam as soon as possible! And just you wait, before you know it I'll be the Hokage handing out your missions!" Naruto proclaimed.

Shinji chuckled as he handed the self-proclaimed future Hokage a bento and they left the apartment, Naruto to the academy and Shinji to the Hokage Tower. Truthfully Shinji really did believe that Naruto could become Hokage. He had the potential; he just had to tap into it.

When Shinji reached the Hokage Tower he was directed to the Hokage's office who was waiting for him.

"Ah, Shinji-kun it's good to see you." Said the aged Hokage whom Shinji had come to see as a grandfather alongside Naruto.

"It's nice to see you to Ojisan." Replied Shinji. "I hear you have a pretty important mission for me."

Sarutobi nodded. "That I do Shinji. This is a long-term spying mission that I feel that you are more suitable than anyone else." He said as he took out a manila folder that contained the specifics of the mission. "I will assign two other Chuunin who will help you and one Jounin who will act as team leader in case of emergencies, but you will actually be leading the mission. One of the reasons that you will lead is because you will be in charge of all the information. Also this will be good experience for you as I doubt you will run into any trouble. The time table for this mission calls that you will be finished in six months."

"SIX MONTHS!?" Shouted Shinji. "Hokage-sama that has to be some kind of mistake. Even border patrol missions don't last that long. And normal spying missions only last 2-3 weeks tops. The only reason Jiraiya stays out that long is because he usually only comes back when there's something to report." He said listing off the various reasons why that had to be wrong.

"Sorry Shinji but there is no mistake, and this will not be a normal mission." The Sandaime answered as he pushed the folder forward.

Shinji opened it and rifled through the first few pages. On top was his shinobi profile, followed by his teammates, the Chuunin being Kotetsu Hagane and Izumo Kamizuki, and the Jounin being a man named Yamato. But under that were files of the four people that did not look anything like their shinobi profile. Looking at his file he noted that it had all the normal information but also included a listing of schooling that he never had. When he noted the listed home address his eyes widened. Osaka, Japan is what it said. "Japan?"

"Yes Shinji. What makes this mission unusual is that it is outside of the Elemental Countries. Thanks to Jiraiya's spy network and Genjutsu we have been able to able to keep a false set of records that show a false life of you living in Japan. Since these are based on your original records, they will stand up to the greatest scrutiny from anyone. Which is more then we can say for the records we have for our other shinobi. Plus since you were born and raised for the first few years of your life there you will have an easier time blending in." Sarutobi explained. "You will gather information through the network Jiraiya set up years ago. Kotetsu, Izumo, and Yamato will contact informants outside of Japan and send the information to you, at a set time you will summon a toad and hand a report to it. Later Jiraiya will be given that report and he will supply it to me if he sees anything important. Are there any questions?"

"Yeah. You really expect me to be gone for six months?" Asked Shinji. "What about Naruto."

"Iruka can handle Naruto just fine and you know that. Besides he's old enough to watch out for himself."

"Yeah, but what will Iruka do when Anko decides that Naruto must die for some transgression. He's not exactly very stern with her." Shinji said as he remembered the one time they had pranked the snake kunoichi and how Iruka had not been much help. Shinji had long suspected that the two had a crush on each other.

"We'll cross that bridge when he get there, but this mission is too important."

"Then answer this Hokage Ojisan. Since when is it so important to have someone like me gather information of the outside world? It was never important before."

The Hokage took out several more folders and scrolls. "Recently our spies have reported that the UN military forces as well as the JSSDF have started mobilizing in Japan. Also our spies in NERV the organization that replaced GEHIRN have reported that they have been more active lately. As if they were preparing something." He said as he opened them up showing photos of various military vehicles as well as logistics reports. There were no photos of what NERV is doing. "We don't know why they are doing this as most of the informants don't have a high enough ranking position to give us much. But what we do know is that they are mobilizing for the same reason. Whatever this threat is the UN, JSSDF, and NERV all plan to fight it. Only NERV has gone and built some new type of weapon called an Evangelion to fight it. All information on the Evangelion is top secret and we have almost no information on it. What we do know is that that there are multiple units and they need children pilots."

Shinji raised an eyebrow in curiosity at that. What kind of organization would send children to the front lines? Sure they did that in the shinobi world, but they received extensive training and even then didn't go on the serious missions until they reached a rank that showed they were ready. "Sigh…When do I leave?" He asked.

"Tonight. That should give you time to pack your things and say your goodbyes."

* * *

"You're going to be gone six months!?" Exclaimed a dismayed blonde. "But you'll miss my graduation!"

"Sorry Naruto, but those are my orders. Besides Iruka will still be here." Shinji apologized as he packed up what belongings he needed. Setting a supply of emergency rations on top of an open scroll inside and intricate series of seals he brought his hands into the Ram seal and said, "**Fuuin**," sealing the food into the scroll. That scroll was one of many that possessed everything from Shinji's camping gear to spare weapons to techniques he wanted to learn. He had enough to invade a small country. But hey, he was going to be gone for six months and it wouldn't be easy to replenish his supplies in the outside world.

"But you promised to teach me how to walk on water this week. Ero-sennin said he wouldn't teach me the Rasengan until I know how to do that."

"I'm sure Iruka can teach you. He is a Chuunin just like me and he's very good." Shinji said as he put on his backpack. "Listen, the months will fly by and I'll be back before you know it." He assured as he headed out the door. "See you in a few months bro."

"Yeah and when you do I'll be a Chuunin like you!" Naruto shouted back, making Shinji laugh.

"Yeah, sure you will."

Within a few minutes Shinji found himself at the gate where his teammates were waiting. Izumo with his hat. Kotetsu with that wrap on his face. And the unknown Jounin Yamato who wore a shinobi helmet that protected the sides of his face. When Shinji arrived Yamato spoke up. "Is everyone ready?" The Chuunin nodded in the affirmative. "Alright, then let's go." He said as he turned and walked out the gate followed by the Chuunin.

* * *

"Man it's hot!" Complained Kotetsu as he fanned himself off with a paper fan, his normal Chuunin uniform discarded in favor of a white tank top and loose shorts. He laid sprawled out on the sofa of the apartment that were renting for the extent of their mission.

"Ya know, I went on missions to the deserts of the Land of Wind and I was perfectly fine but this place is torture." Said Izumo who was similarly dressed, sitting on a chair waiting for the moment when the rotating fan would pass over them.

"Actually the temperature in the Land of Wind far surpasses Japan. The source of your discomfort is the humidity which was usually very low back home." Explained Shinji who, being more comfortable then his companions since he already knew the climate, was dressed in a school uniform that was far from standard. For one thing he always wore his open Chuunin vest over the shirt. The pants looked normal but had been re-stitched so it would allow the maneuverability that was required of a shinobi. When he wasn't at school he wore his supply pouch and kunai holster. And he always wore his hitat-ate somewhere on his person. Today it was on his left bicep.

It had been a month since the Shinobi arrived in Osaka. They immediately moved into an apartment that was right next to the one owned by the very man Shinji was supposed to have lived with before he started training with Jiraiya. Of course to help keep their cover they had to enroll Shinji in school where they had used a subtly Genjutsu that made everyone believe that Shinji had always been in there, he was just quiet and didn't interact much with others. The 

Genjutsu would hold up as long as Shinji didn't really try to bring attention to himself. At first Shinji wasn't too keen to go back to school but it was necessary so he could learn how to use items like computers. Now the three Chuunin were waiting for Yamato to return with the information from the informant in Russia. They had to admit that phones and computers made their job easier.

The three heard the door open and shut and turned their heads when Yamato entered the room, in one hand was the info, the other contained the daily mail.

"Anything interesting?" Asked Izumo.

"The informant did not provide anything we did not already know. However Shinji did receive something in the mail. I took the liberty of picking it up from next door when I saw it." He said has he handed Shinji a large yellow envelop.

Curious has to who would send him something when he practically doesn't exist here Shinji looked at the return address. His eyes widened as he saw it was from NERV and he had a suspicion he knew who sent it. Opening it he let the contents drop onto the coffee table. Most of it were different sets of paper. Some were transportation instructions stating that he would take the train to Tokyo – 2 and then he would be picked up by a Captain Misato Katsuragi who would take him to Tokyo – 3. Accompanying those was a photo of a very pretty woman with purple haired tied into a ponytail, while wearing a tight pink tank top with cut off jeans. Her pose was rather flirtatious and it did not help that there was an arrow that said 'Look Here' pointing at her generous cleavage. But Shinji's attention was drawn to a small postcard sized piece of paper. The letter head said it came from the office of Commander Gendo Ikari. There was only one word written on it, "Come." Shinji's eyes narrowed in anger at the audacity of the man. He unconsciously started letting off a bit of unfocused killing intent.

"Hey Shinji, you ok?" Asked Kotetsu as he noticed the killing intent coming from the younger Chuunin. Shinji didn't say anything and just pushed the papers towards the others. Looking them over, it wasn't hard for the older shinobi to understand why Shinji was angry. They had been told about his past here in Japan as they traveled here.

"So what are you going to do?" Asked Yamato. Shinji was still in charge and this was not the kind of situation where he could step in and assert Jounin authority.

"As much as I would like to ignore anything that man sends, this is a good opportunity to get more information out of NERV. So for the good of the mission, I will follow the instructions in those orders and your three will relocate to Tokyo – 3." Said Shinji.

Yamato nodded in approval at the plan. Izumo also showed his support, but in a different way. "Hey look on the bright side. At least your ride is hot." He said, sounding a lot like a certain perverted Sannin as he picked up the picture and started ogling the figure on it. Everyone else sweatdropped at this.

* * *

**Author's Notes:** This is my second Eva fic and is another side story that I will work on when I feel like it. I had never seen this crossover before and decided that I would give it a try. Anyone familiar with my Naruto stories will have noticed that I am writing the names in the English format of given name first then surname. That is something that I will always do in any Eva fic I write.

Next chapter is Shinji's introduction into NERV as well as the fight with the Third Angel. I will also introduce Shinji's first love interest. Can you guess who?

**Please Read and Review.** I love reading any comments people have to say about my stories and it helps inspire me to write.


	2. Arrival at NERV

**Shinji: Path of the Shinobi**

**Disclaimer: **I do not own Evangelion or Naruto

"Hello" – Speaking

'_Hello_' – Thoughts

"**Hello**" – **Demon/Boss Summon Speaking/Techniques**

'_**Hello**_' – **Demon/Boss Summon Thoughts/Techniques**

* * *

**Chapter Two: Arrival at NERV**

"We're sorry, but due to a state of emergency in the Kanto and Tokai regions all phone lines have been shut down. Please hang up and find the nearest shelter until the emergency is over. Thank you." Said the recording on the other end of the phone.

Shinji sighed. '_Just great._' He thought. He knew that going to see his father was a bad idea and it seemed some cosmic force in the universe was trying to prove it to him. Here he was in Tokyo-2 waiting for his pickup, who was several hours late he might add, and a state of emergency gets called. That explained why there was no one around as they must have been evacuated earlier, but he had to wonder how they had missed him. Maybe it had something to do with the suspiciously empty train he rode here. And with the phone lines down he couldn't call anyone so no one knew of the predicament that he was in.

Shinji contemplated just running back to Osaka, even if it would take a day or two at top speed. But he would just be going back to an empty apartment as the rest of his team was already in Tokyo-3 prepping to stay there a while just in case whatever it was he was called for took longer than a few days.

As he just stared into space trying to figure out what to do now, he suddenly noticed he wasn't as alone as he thought. Standing at the far end of the street was a blue haired, red eyed girl wearing a blue green school uniform. Looking at her Shinji had to admit that the girl was rather cute, but there was a nagging at the back of his mind that something about her wasn't right. If he wasn't so focused on how pretty she was he might have remembered that outside of the Hidden Continent features like blue hair and red eyes were not normal. Now he just took those in without a second thought. After all there was a girl in Naruto's class with pink hair, and Kurenai-sempai had red eyes, so to him they weren't odd at all. But there was still something not right about her.

The ground shuddered and Shinji's attention was directed towards a flock of birds whose sudden departure startled him. Turning back to the girl, Shinji was surprised to see that the girl was gone. '_What the? Where did she go? There's no way she could have moved so fast without being a kunoichi. Unless she was never there to begin with. Genjutsu? But there has to be someone around to cast the illusion, and as far as I can tell I am the only one here._' His musings were cut short by another tremor. '_What is going on?_' That question was answered only a second later as the source of tremors appeared from behind a mountain, accompanied by a couple of VTOLs.

The giant was vaguely humanoid in shape, but it had no head or neck, its bird like face being on its chest in between its massive shoulders. Just above a red orb.

Shinji wasn't very familiar with modern weapons like those jets, but he could honestly say that he was not surprised to see that all of their bullets and missiles were having no affect on the green monstrosity.

'_Seriously, what is that thing? A Bijuu? No, it doesn't have a tail._'

Information on the Bijuu was hard to come by in Konoha and Shinji only knew about them from the book he accidentally found in the library as he was searching for something else.

But even if it wasn't one of the legendary tailed beasts, the creature was putting out an amazing amount of chakra. There was no doubt in Shinji's mind that this thing was a demon. If the Kyuubi's attack on Konoha was anything like this then Shinji had to wonder how the Yondaime defeated it.

It seemed like the giant grew annoyed with gnats that were pestering it. Raising its arm a lance of chakra sprung forth and with amazing accuracy ripped through one of the VTOLs. The machine was split into two halves, each tumbling to the ground. One straight for Shinji.

His training taking over Shinji did a number of back flips in order to avoid the wreckage, unaware that he had an audience.

The screeching of tire wheels was all the warning he got as a blue Aspin Renault skidded across the pavement to a stop, nearly hitting him in the process.

"Get In!" Shouted the purple haired driver who had been sent to pick him up.

Shinji didn't waste any time as he leaped through the open window of the passenger side so fluidly it would have made the Duke Brothers proud.

No sooner was the boy in the seat when Misato gunned the accelerator, speeding off away from the demon.

"Whew." Breathed Misato when the monstrosity was slowly getting smaller in her rear view mirror. "Sorry about being late Shinji. I'm Captain Misato Katsuragi, hope you weren't waiting long." She said to her companion, who was keeping an eye on the distance between themselves and the demon. "By the way that was some pretty fancy acrobatics out there. Where did you learn it?"

"Huh? Oh, it was just something that interested me so I practiced it on my own." Deciding to change the topic he asked. "So what was that thing out there Captain Katsuragi?"

"Please call me Misato, and that Shinji was an Angel." Misato said in a hard voice. Obviously not the best subject of conversation with her.

But still an Angel? Shinji was familiar with the term as Angels were somehow represented in just about every religion known to man. And if there was a shred of truth in those religions then that thing was about as un-Angel like as possible. Unless it was supposed to be a fallen Angel, but aren't those also called demons?

"You know Shinji; you seem pretty calm considering the situation." Misato commented to her passenger drawing him away from his ponderings.

"Trust me Misato, I am far from calm. But there is little point in physical panicking. At least not yet." Responded Shinji. He was pretty good at keeping his emotions from showing. Didn't help much the first time he was in a fight, or after his first kill, but he eventually learned that experience was the best teacher.

The ride out of the city was pretty quiet after that, if you didn't count the roaring engine and the tires. At least until Shinji noticed something going with the Angel battle. "Uh Misato? What is the military doing?"

Misato stopped the car and took out a pair of binoculars. After two seconds her eyes bugged out. "Oh No! They're bugging out! That means they're using an N2 mine!" She shouted. "Get Down!" She cried as she threw herself to cover the boy just before the shockwave from the explosion struck the car, forcing it to tumble around before stopping on its side.

After the car came to a stop and the shockwave stopped Shinji climbed out of the car from the driver's side window, rubbing his head in pain. "Ow. You all right Misato?" He asked as he helped the purple haired woman out of the car.

"Yeah Shinji I'm fine." She said while dusting herself off. Then Misato noticed the condition her car was in. "NOOOO!! My Car! I Still Had 33 Payments Left!" She wailed to the heavens.

Shinji didn't know what she was so upset over. Sure it was dinged up, but from what he knew about cars, which was very little, it would still run.

After Misato's cries of despair ended Shinji helped her flip the car back onto its wheels for which she complimented on his usefulness. However when she attempted to restart the car a new problem became evident. The battery was dead.

"Damn It!" She exclaimed banging on the steering wheel and was about to have another bout of tears when Shinji tapped her shoulder.

"Um, Misato. Could we get another battery from over there?" He asked pointing to an auto parts store that was placed conveniently nearby.

Misato smiled, she had a feeling she was going to like this kid.

Ten minutes later the two were back on the road.

"Misato, are you sure we need that many batteries?" Shinji questioned as he looked at the lifetime supply that currently resided in the back seat.

"Don't worry." Responded the klepto-driver. "It's an emergency."

Shinji rolled his eyes but he could understand why she did it. She was taking advantage of the situation to her benefit just like any good shinobi would do. Didn't mean he approved but it wasn't his place to judge.

As the drive continued Misato began talking on her cell phone. "Yes, don't worry his safety is my top priority." "I'd like a train car prepared for us. An express of course."

With the call finished she turned to her passenger. "Shinji, do you have the ID your father sent you?"

Shinji took out the ID that had been sent with everything else. The ID was for the organization called NERV. An organization that Konoha knew little about. Shinji began mentally reviewing what he did know to prepare himself for what was to come.

NERV was once an organization called GEHIRN, until five years ago when it was restructured into NERV. Virtually all personal, equipment, and facilities were transferred over to the new organization. Among the few personal that did not transfer over was the notable exception Dr. Naoko Akagi, GEHIRN's head technician and creator of the Magi supercomputers, who committed suicide no less than a day after her ultimate creation was completed. Several days before the transfer.

The organization is an international UN funded organization with facilities all over the world on every major continent. The First branch resides beneath the city of Tokyo-3, formerly the city of Hakone which was reconstructed to serve whatever NERV's purpose, whatever that is. The city was brought online and was officially renamed at the same time GEHIRN became NERV.

Although GEHIRN and later NERV was established and run by civilians, the UN has given the command structure military authority and titles and is treated as a separate military entity not associated with any government. The third highest person in NERV is Captain Misato Katsuragi the Operations Director. Above her is Deputy Commander Kozo Fuyutsuki, a former university professor at his mother's alma mater. And finally at the top of the command structure was his father Commander Gendo Ikari. However Gendo must also report to a group called the Human Instrumentality Committee who oversees NERV for the UN.

There was also a civilian group of scientists and technicians headed by Dr. Ritsuko Akagi, daughter of Naoko Akagi. While she was not quite the equal of her mother when it came to programming or system designs she came close and possible surpassed her when it came to biology and medicine.

Officially NERV is supposed to be a secret organization known only to the UN, the governments that are a part of the UN, and said government's military that NERV is supposed to be working with for some common goal. However what that goal is unknown to anyone outside of the organization except for the topmost governmental officials and military generals. And they weren't saying anything. Nor could Konoha gain the info through any of the informants working for NERV because of their fear of Section 2, the security and counter-intelligence forces of NERV who keep an eye on just about everyone to make sure there are no security leaks. Because of them all of the informants couldn't risk providing information that was too important so as not to raise any flags.

But one last bit of important information was that of the Evas and their pilots the Children. The designated First Child is one Rei Ayanami. All public records concerning her are classified to all but the highest members of NERV. And the Second Child is Asuka Langley Soryu, a German girl that is one-fourth Japanese whose mother was one of the top scientists at NERV's Third Branch in Germany.

Maybe it's time to try to get some more. "What is NERV?"

"Hmm, Oh right." She reached over and opened the glove compartment pulling out several books and pamphlets and handing them over to Shinji. The largest of the books had the word NERV on the front with the symbol of a fig leaf surrounded by a border caption of, 'God's In His Heaven…All's Right With The World.'

"NERV is my father's organization?"

"You don't know what your father does?" Asked a genuinely surprised Misato.

Shinji shook his head. "All my teacher told me was that it was important for the fate of mankind."

"Is that what you think?"

Shinji mentally sighed. Well might as well giver her something, then she might open up and give him what he wanted. "I don't think my father really cares about me." He said in a despondent voice.

"Sounds like you and I are a lot alike." Said Misato. "I didn't get along with my father either."

While he had been musing and then talking with Misato, the car had long since been parked and was now being moved underground. Deep underground. Very deep underground. Where were they going?

That's when the tunnel ended revealing what lay beneath.

"Whoa." Exclaimed Shinji. "It's a Geo-Front." He had read about it in the reports but they don't do the magnificent cavern justice.

"That's right." Said Misato as she pointed out the large pyramid construct next to an artificial lake where a naval destroyer sat. "And that is the secret headquarters of NERV, a man-made fortress against the Angels, and our last hope for humanity."

Shinji would admit that it the vista below him certainly did inspire hope.

* * *

"Yeerrgg! This is why I hate wearing skirts in this place." Complained Misato as the change in air pressure from the opening of the automated doors caused her dress to flutter about.

Shinji didn't bother commenting on what color panties she was wearing in favor of learning the layout of NERV. There was just one problem. "We've been through this hallway two times already."

"Uh, well don't worry. These walkways were made to be used after all."

"You're lost, aren't you?"

"Shut up! I know exactly where I am going." Said the woman looking at a map.

Shinji looked to the side and stopped. "Isn't that an elevator?"

Misato stopped and looked at the double doors her charge had pointed out. Then she checked her map to confirm their position. Then back to the elevator. Then back to the map again. And once more turning to the elevator. She finally nodded in conformation. "See I told you that I would get us there." She proudly stated as she strode forward.

"We only had to go by it three times for you to notice it." Shinji muttered under his breath. "What was that?" Asked Misato in an oh-so-sweet voice that reminded him too much of another certain purple-haired woman who happened to have deadly proficiency at throwing sharp implements of pain and who frequently threatens him through the use of possible neutering. Where was that blonde haired decoy when you really needed him?

"Nothing, nothing." Shinji hastily said.

"That's what I thought." Misato smugly responded. That smug grin of her quickly turned to one of embarrassment as the elevator door opened, revealing the form of one annoyed Doctor Akagi. "Uh, heh heh. Hey Ritsuko."

"Honestly Misato. You've worked here how long and are still getting lost?" Huffed the annoyed faux blonde. Glancing over she noticed Shinji just behind her. "So this is the Third Child?" She said looking the boy over as if he was some new piece of equipment.

'_Third Child?_' Thought Shinji, barely able to keep his face from reacting. '_Child is the term for the pilots of the Evas. Do they want me to pilot?_' In Shinji's mind, things were starting to make sense. Such as why his father summoned him. '_Well no need to let them know I know._' "Hello, I'm Shinji Ikari. It's nice to meet you." He greeted with a bow.

"Hello Shinji. I'm Ritsuko Akagi, Director of Project E, and head of the technical division. I'm pleased to meet you." She responded friendly as she stepped aside to allow Shinji and Misato aboard the elevator.

"So tell me Dr. Akagi, is what your wearing the standard woman's uniform in the technical division and if so how do I join?" As Shinji with only a mildly perverted smile on his face as the elevator descended into the bowels of NERV. Hey when you are raised by a self-proclaimed super pervert some of his personality will rub off on you no matter how much you fight it.

Ritsuko blushed as she tightly closed her lab coat, the only thing she was wearing over her one-piece bathing suit. "I'm having a hard time seeing the family resemblance to the Commander." She commented to Misato.

"Yeah," Misato grinned humorously in agreement, she knew she was going to like working with this boy. "He really is nothing like his father, being all polite and friendly. Nothing at all like the gruff Commander."

* * *

The trio had gotten off the elevator and was now traveling upwards on a massive escalator. Shinji absently wondered why they had even bothered to use the elevator of they just had to go up again. As they traveled upward an announcement came over the intercom. "_Battle Stations, Level 1. Prepare for ground intercept._"

"There they go." Muttered Misato in a tone saying that she had expected the message. "How is Unit 01 coming along?"

"It is currently undergoing refrigeration using the B-type equipment." Informed Ritsuko casually.

"Will it really work? It's never worked before." For the first time since he met her Shinji heard something akin to worry and perhaps even desperation within her voice. He had heard fear such as when the N2 mine was about to be used, but fear and desperation were two different things with the latter being the worse of the two to have.

"The possibility of activation is 0.0000000001%." Stated the scientist. "We refer to it as the 09 system."

"So does that mean it doesn't work?"

"Don't be insulting." Shot Ritsuko actually sounding insulted. "It's 09, as in an Oni. A Japanese devil." Unseen behind the book he was reading Shinji's eyebrows raised in confusion. How did that make any sense to the blonde doctor? If his math was right then there was a 1 in 1 trillion chance for this Unit 01 to activate but what did that have to do with Japanese mythology? Well, maybe he'll figure out the thought processes that lead to the nickname later.

"Well, I suppose it's a bit late to say 'Sorry it doesn't work.'" Said Misato jokingly, seemingly back to her old self.

After the long escalator ride (Shinji half expected for them to back up on the surface, but apparently the place was larger than he thought) only to arrive at a lake of an amethyst liquid which they used a motorized raft to cross to a metal construct that rose out of the substance.

Once the boat was moored Misato and Ritsuko lead Shinji through the constructs open doors into a dark room where the only light came from outside. Once they were inside the doors shut plunging the place into impenetrable darkness. Shinji's instincts immediately screamed at him to move to prevent himself from being ambushed in potentially hostile territory.

Then the lights switched on and Shinji was confronted by the massive horned face of a creature that could only be described as an Oni. The face of Unit 01. Shinji was stunned as feelings washed over him. He knew he had seen this thing before long ago, before he met Jiraiya, but he couldn't remember where or anything about it. "What is this thing?" He asked quietly.

"This Shinji is mankind's ultimate fighting machine. The synthetic life form known as Evangelion Unit 01. Built here in secret it is mankind's last hope." Explained the doctor.

Now Shinji understood. This Evangelion was a weapon constructed to fight the demon, that 'Angel' up on the surface. "And this is what my father has been working on?"

"That is correct." Said a voice from above.

Looking up Shinji saw a man he had not seen in ten years, whom he was related to by blood only. The man who abandoned Shinji during a time of emotional fragility after his mother's death. But deep down he there was a piece of his soul that thanked Gendo for what he did. Because if it had not been for Gendo abandoning Shinji then he would have never met Jiraiya, his brothers Naruto and Iruka, and he would never have become a shinobi of the Leaf. However that piece was so far down not even Shinji knew it existed.

Gendo's observations of his son surprised him somewhat. Not once had he had any sort of contact with Shinji beyond the annual reports from the caretaker he had left Shinji with. Not even at Yui's grave. And all the reports indicated that Shinji was quiet, meek, doesn't stand out from the crowd, and avoids confrontation. The boy below him didn't fit that description.

His clothing, from the vest to the headband tied around his arm to the sandals, worn with a standard school uniform would stand out in a crowd. His facial expressions showed not a hint of meekness but instead defiance to Gendo. It might be more difficult to control the boy then he thought. But that was alright; even if that was the case he still had his trump card. "It's been awhile Shinji." The boy's slight scowl hardened, unbeknownst to Gendo Shinji was sorely tempted to test the strength of the glass that separated them with some kunai and explosive notes. "We're moving out."

"Moving out!" Exclaimed Misato. "But Unit 00 is still in cryostasis." It would be impossible to get the prototype Eva ready to face the Angel. Then with a gasp she realized the Commander's intentions. "Wait! You're going to use Unit 01!"

"There is no other choice." Said Ritsuko, clearly pre-informed and prepared for this course of action.

"But Rei is in no condition to fight! We don't have a pilot!" Argued Misato.

"We just received one." Countered Ritsuko.

"You can't be serious!"

Ritsuko ignored that last comment in favor of turning to Shinji. "Shinji Ikari, you will pilot Unit 01."

"But even Rei Ayanami took 11 months to synchronize with her Eva! It's impossible for him to do it, he just got here!"

"He just has to sit in the seat. We don't expect anything more than that."

"But…"

"Listen, defeating the Angels is our top priority. If we have someone who has even a chance at synchronizing with an Eva, then we have to risk it no matter the cost. You understand that don't you Captain Katsuragi?" Ritsuko's use of Misato's rank was a clear indication that the discussion was over.

Made even clearer when Misato replied with a resigned, "Yes Ma'am." However the argument was only over for the staff member of NERV.

"Now Hold On!" Shouted Shinji grabbing the attention of all the NERV personal. "You two keep talking as if I don't have a choice in the matter, and it's starting to get on my nerves. And you old man!" He shouted as he turned his face upward towards his father. "The first time you contact me in 10 years and it's to pilot this thing right?"

"That is correct."

"Well you can forget it. I don't take orders from you or anyone else here." With that he turned to leave only to be stopped by a hand upon his shoulder. Looking up he saw the hand belong to Captain Misato Katsuragi.

"Shinji please. You have to pilot it." She begged. "If you don't and the Angel destroys NERV then a lot of people will die. The people of Tokyo-3, of Japan. The entire world is in danger because the Angels won't stop until all of humanity is dead."

That made Shinji pause. He was a shinobi and no stranger to death and destruction, but he wasn't the kind of person that would ignore the senseless killing of others around him, especially if he had the capability to stop it no matter how slim the chance. And even if he didn't care anything for strangers there was the fact that his teammates were in the city above and as a Shinobi of Konohagakure no Sato he could not in good conscious leave behind his comrades to certain death.

While Shinji was contemplating on what he should do, Gendo decided it was time to play his trump card. Activating the video screen he spoke to his Sub-Commander. "Fuyutsuki, I want you to wake Rei."

"What?" Fuyutsuki gasped in surprise. "Is she in any condition to pilot?"

"She's still alive isn't she?"

Back down on the lower level Shinji was about to declare his final decision when he heard Gendo speak up again. "There is no time for this. Dr. Akagi reconfigure Unit 01 for Rei."

Shinji sighed. '_Well, looks like they have another pilot after all. Guess the best course of action is to find my team and get back to Konoha. I doubt that whatever this Angels are going to do to the rest of the world will affect the Hidden Continent. Second Impact didn't._' The sound of doors opening behind him alerted Shinji to the arrival Rei. Shinji turned wanting to get a glimpse of the mysterious First Child. What he saw both surprised and horrified him.

It was that girl! That girl that appeared and disappeared out of nowhere. But she was different this time. She was being wheeled in on a gurney by a medical team and from what Shinji could tell from his limited medical knowledge she was not in good condition. Her right arm was in a caste while her left arm, upper right arm, head, and left eye were all bandaged. And from the looks of things she was having trouble breathing as well.

"Rei, the spare is useless. You will pilot." Commanded Gendo.

"Yes Sir." Gasped the girls as she attempted to raise herself off the gurney. A job her trembling limbs were unable to accomplish. Before her body gave out she felt a strong pair of hands grab hold of her, one on her shoulder the other one supporting her back, and gently yet forcefully pushed her back down. Looking up she saw a young brown haired youth with piercing blue eyes that had pushed his way past the medical personal that were in charge of keeping her alive. A gentle smile on his face as he quietly spoke to her.

"Be still and lie down. I'll take care of it." She would have struggled against him, telling him that she must do as the Commander says but she simply lacked the energy to do so. She watched as the boy turned his head to the Commander the two giving each other unreadable expressions, neither willing to back down. Who knows how long they would have kept this up, had the Third Angel not reminded the world of its presence.

An explosion sounded above and the world shook. Shinji snapped his eyes upward where he saw the falling debris that fell from the ceiling, and he wasn't the only one to see it. The medical team saw it and ran away, leaving their patient to die. Grabbing Rei, Shinji picked up the red eyed girl bridal style and leapt away, narrowly avoiding the debris crush the gurney like tin-foil and surprising those who witnessed with his physical prowess. But as he landed a second explosion rocked the world and Shinji lost his footing.

Despite being racked with pain Rei stayed conscious and watched as a steel beam fell from above. In mere seconds everything would be over for both her and the Third Child. But fate had other plans.

The eyes of Unit 01 flashed with an inner light and a monolithic hand blocked the debris a mere second from impact. The debris bouncing away harmlessly like pebbles off its armor.

"That's not possible!" Exclaimed Dr. Akagi, seeing but not believing what Unit 01 had done. "The Entry Plug hasn't even been inserted!"

Misato just stared in astonishment at the boy. How he had so effortlessly picked up Rei and jumped with a speed to avoid being crushed and how for the first time she was aware of Unit 01 ever activating, seemingly in response to the danger of the same boy.

Shinji looked to the girl in his arms, still conscious and trying to keep herself from crying in pain. Shinji's heart went out to the girl, still struggling to remain awake. When he had seen her try to obey the commands of his father only moments ago despite the condition her body was in, it had reminded him of the horror stories he had been told of the old ROOT division whose members were trained from infancy to obey their superior's orders and to carry out the mission no matter what. Even if their body was on the brink of death, even if they had to kill a comrade they would accomplish their mission or die trying. And Shinji couldn't let the First Child continue like this.

"I'll do it." He announced in a voice loud enough for his father to hear. "I'll pilot the Eva."

Behind the glass window separating him from the room his son was in, Gendo smirked. It would seem that despite the discrepancies in the reports, he could still manipulate Shinji to do what he wanted.

A new gurney was brought out and Misato helped Shinji to place Rei gently on it. Once the medical team was walking away with the girl Misato was about to leave to attend to her post when she saw Shinji remove the metal plated headband wrapped around his arm. "Shinji, if you're worried about your headband getting ruined in the fight I could keep it safe." She offered.

"No thanks." Responded Shinji as he retied the headband around his forehead and then pointed at it with his thumb. "This hitat-ate is a symbol of what I believe in and what I fight for. It is a reminder of who I am and what I must do to protect my friends and comrades."

The speech confused Misato, but she understood the gist of it. After all, she would never be willingly parted with the cross that is the only memento of her father that she had.

* * *

Shinji sat in the entry plug, meditating while the NERV crew went through the process of bringing Unit 01 out of cryostasis. To Shinji's ears it sounded to consist mostly of releasing the locks and bolts that supposedly restrained the Eva and kept it from moving. Yeah right. If that little demonstration earlier was any indication the chains were merely to bring a sense of safety to those that have to work with the behemoth.

However when he heard the words "_Flooding the entry plug_," over the radio he grew a little worried. And when the Eva's cockpit started filling with a yellow liquid he grew really worried.

"Hey! What's going on!?" He shouted angrily as the substance rose above his knees and quickly reached his head forcing him to hold his breath as he became submerged.

"_Don't worry._" Said Dr. Akagi over the radio. "_It's LCL and it's oxygenated so when it saturates your lungs it will supply oxygen directly to your blood._"

Shinji knew that he couldn't hold his breath forever and he might as well take the plunge. Opening his mouth he emptied his lungs of oxygen and inhaled the LCL. Mentally he shuddered at the taste. '_Even Anko, with all of her strange tendencies, would not enjoy this._' He thought, out loud he said. "You know you could have given me a bit of warning before you started filling this thing up."

"_Sorry, slipped my mind_." Responded Ritsuko dismissively, distracted by the readings on the monitors. The data feedback from the Eva was looking good so far.

"_Connecting secondary contact._"

Shinji blinked in wonderment as the LCL suddenly lost its clear yellow color and became invisible to his eyes. Then the interior of the entry plug shifted and became a rainbow of colors as tiny sparkling lights similar, to hundreds of diamonds, shimmered about him. Finally the interior of the entry plug became a view of the area around the Eva, as seen through its eyes.

Back in Central Dogma Lt. Maya Ibuki was reporting the condition of the Third Child to the head of scientist of NERV. "Bidirectional circuits are open. Synchronization ratio is at 41.3%. Harmonics seem to be normal."

"Incredible." Breathed Ritsuko at the sight of someone bypassing the absolute borderline and actually synchronize with an Eva on their first attempt. Turning to Misato she gave the OK.

"Begin launch sequence!" Commanded the purple haired Operations Director.

The Eva cage became a hive of activity as the primary locks, secondary locks, and safety restraints that held the purple titan in place her removed and the Eva was moved to the launch pad.

Once in place a series of doors opened up and cleared the path of the catapult. Everything was ready.

"Eva Launch!"

The G-forces pushed Shinji back into his seat as the catapult rocketed the Eva upwards towards the surface. And just as suddenly as it started, it stopped with a slight jerk, the motion absorbed by the LCL to prevent injury to the pilot.

But that was a small comfort to Shinji as he saw the Angel appear around the corner of the building. Apparently whoever was running this show had decided that they would send Shinji into a direct line of interception against the Angel, not giving Shinji a chance to practice moving Unit 01. If he can move it that is.

To make matter worse it looked like the Angel had gotten larger since Shinji had last seen it several hours earlier. At the very least it had broader shoulders and now had two skull faces, one overlapping the corner of the other.

"_Are you ready Shinji?_" Asked Misato in a concerned voice over the radio.

"As I'll ever be." Responded the shinobi.

"_Final Safety Locks Release!_" Misato shouted switching back over to Operations Director mode. "_Evangelion Unit 01 Move Out!_"

The locks that held Unit 01 to the catapult released causing the Eva to slump as the support was removed.

"_Shinji, just focus on walking for now._" Advised Ritsuko.

Shinji followed the advice and concentrated on the action of walking without actually moving his legs. In response Unit 01 took a slow almost halting step forward. Which was enough to cause a great deal of excitement in Central Dogma. "_He's walking! He's actually walking!"_ Then to the surprise of the command staff and the bridge bunnies Unit 01 took a more confident step…backwards.

"_What are you doing Shinji? The Angel is right in front of you!_" Shouted Misato.

Shinji frowned thinking that what he was doing would be obvious. "Misato I have no intention of fighting the Angel until I am sure I can properly fight with this thing." Explained Shinji as he took another step back, then forward as he moved his arms. The Angel for the most part seemed content to let Shinji keep practicing for the moment.

Whether it was because the Angel was waiting for an opportune moment to strike or was simply confused at how to deal with an opponent of equal size Shinji didn't know, but he wasn't about to look a gift horse in the mouth. Every second the Angel waited was another second that Shinji used to his advantage as he went through slightly more complex exercises. Too bad not everyone was as patient at the Angel.

"_We don't have time for that!_" Shouted Misato. "_If that Angel gets to us then all of mankind will die!_"

'_Way to put on the pressure Misato._' Thought Shinji as he resisted the urge to roll his eyes. "Listen Misato, I know that the circumstances are a little dire and that you sent me out here with no real hope of being able to pilot the Eva. However I can make it move and for some reason Angel is giving me time to practice. I'm going to make full use of however much time I have because if I can't move then I can't fight and if I can't fight then this ultimate weapon of yours is nothing more than a wall. And every wall no matter how strong will eventually crumble and fall. As a military Captain you could know that."

Misato flinched at the reprimand that came from the pilot supposedly under her command. She did know that. One of the basic rules of strategy was that the best defense was a good offence. But the desperation of the situation of having only one untrained pilot and her own personal feelings had clouded her judgment for the moment. The odds must have been a thousand to one that Shinji could actually get the Eva to move much less fight. Yet it seemed that Lady Luck was smiling on Shinji, NERV, and the human race in general today.

Moving the Eva, Shinji discovered, wasn't the hard part. No the hard part was the synchronization ratio. The higher the ratio the more quickly the Eva would respond to its pilots thoughts. And at his current ratio he could move the Eva with increasing fluidity, but his movements were still slow. Too slow for the shinobi's taste. Engaging the Angel with Taijutsu would be difficult and dangerous considering the abilities it had show previously against the JSSDF.

Speaking of engaging the Angel seemed tired of waiting as it strode confidently forward, arms reaching out to demolish this latest barrier in the path of its mission. Shinji saw it coming and stopped his practicing. Not particularly interested in a test of strength he ducked beneath the reaching arms, his lack of speed augmented by the Angel's inability to anticipate.

Shinji sent one of Unit 01's massive fists in a devastating punch toward the red orb on the Angel's chest, a spot that just screamed 'weak vital point' and hoping to finish this fight with one blow. However the titanic fist that had enough power to demolish a building was stopped by a barrier of orange light in the shape of hexagons. Shinji's surprise left him open as the Angel smashed its arms against him, sending Unit 01 flying into a nearby building, obliterating the mass of steel and glass.

"Uhhh." Groaned Shinji, the phantom pain making his head ring. Refocusing himself Shinji's eyes widened as he saw the Angel's outstretched hand glow. Remembering the VTOL he reacted on instinct rolling out of the way just as the chakra lance slashed through the empty air Unit 01 had just occupied.

Standing back up Shinji noticed that someone in Central Dogma was shouting advice. Dr. Akagi if he was hearing correctly. "_Shinji, the Angel is protected by an AT Field. If you don't create one of your own to neutralize it you won't be able to hurt it._"

'_Make an AT Field?_' Shinji thought incredulously as Unit 01 stumbled backwards to avoid a cross shaped blast of energy fired from the Angel. '_I don't even know what that is much less how to make one._' Unfortunately for the leaf ninja there wasn't any time for the good doctor to explain the process and she had been hoping that his apparent genius at piloting would somehow give him insight.

As it so happens Shinji did receive a form of insight, just not from the Eva. Instead it came from his training. And his training said that it was a living creature even if it was a demon, and like all living creatures with special abilities it was using chakra. And if an AT Field was some natural chakra manipulation trick that could be cancelled by more chakra then did it have to be in the form of another AT Field? Or could it be something else?

If that was true then he had just the jutsu to use. A very special jutsu that he had been very fortunate to be taught and wasn't his to teach.

Standing several hundred meters away from the Angel, Shinji held Unit 01's right arm straight out before it focusing with all his might. If the Eva truly acted as his own body would then that should include chakra and its manipulation.

In Central Dogma the bridge bunnies, Operations Director, Director of Project E, Sub-Commander, and Commander watched in confusion at what the Third Child was doing.

"What is he planning?" Asked the old Sub-Commander, standing faithfully behind and to the right of his superior.

"I don't know." Admitted Gendo Ikari, hands steepled before his face. It was an admission he hated making.

In silence they watched as light blue wisps of energy appeared swirling and growing more numerous until there was a sphere formed from the energy resting in the Eva's palm.

With his technique created Shinji opened his eyes to stare at the Angel before him. Maintaining the focus needed for his jutsu he commanded his Eva to move forward. First at a walk but quickly speeding up to sprinting speed as he charged the Angel.

"What's going on!? Does he have an AT Field erected?" Inquired Dr. Akagi of the bridge bunnies.

"There's no AT Field." Informed Lt. Shigeru Aoba. "But that blue light is giving off similar readings."

As Unit 01 was almost upon the Angel as Shinji thrust the Eva's arm forward with a cry of, "**Rasengan**," and slammed it into the Angel's AT Field.

Everyone waited with abated breath as they watched the two titans clash with both power little understood and power completely unknown.

"Come on, come on." Shinji mumbled under his breath, gritting his teeth in concentration as he pushed the destructive jutsu against the Angel's defensive one. Neither seeming to give way. But then he saw it, his Rasengan edging slowly through the orange hexagons.

"Incredible!" Explained the manga reading Lt. Makoto Hyuga. To him this was almost like one of his favorite comics where the hero uses some special ultimate attack that he shouts the name of against the villain. It was so exciting. But was just as exciting was the information his monitors was giving him. "He's neutralizing the phase space."

Bit by bit the Rasengan pushed through the barrier and when it was halfway through Shinji put all of his effort in one last shove and was rewarded by the AT Field ripping like tissue paper and his Jutsu slamming into the Angel's red core. Shinji continued driving the Rasengan into the sphere, the force of his assault actually pushing the Angel against a nearby building and then pushing that building off its foundation for several meters.

Finally Shinji could felt himself at the edge of his limit for maintaining a Rasengan. He canceled the technique and stepped back from the Angel to assess the damage. Once he had moved away the Angel's eyes and core suddenly glowed and it leaped and folded itself upon Unit 01, encasing the Eva within its body and giving Shinji a perfect view of the spiral etched into the core. In the flash of a moment Shinji realized that his Rasengan had been incomplete by the most crucial step. And then his vision blazed with light and Shinji's world grew dark.

"Shinji!" Screamed Misato as she watched the Angel self-destruct, fear lancing through her heart. As Operations Director the lives of the pilots were her direct responsibility and she had just lost the newest one in the very first sortie.

After a full minute of waiting one of the bridge bunnies spoke up. "Visual has been restored." Reported Lt. Hyuga as the main monitor changed from static caused by the explosion to an image of the city battlefield.

Misato and several others of the command staff breathed a sigh of relief as they saw the Eva was still intact. Its armor was heavily damaged, some so much that it looked like it would have to be completely scrapped and replaced but it could have been a lot worse. "What's the status of the pilot?"

Lt. Ibuki switched the image over to the interior of the Eva making the group of officers gasp at the sight. The interior of the entry plug was lined by a spider web of tree branches. The main part of the tree was formed of the spider web of branches that lined the walls of the entry plug, along which were blooming flowers that looked like lilies, and spreading outward from the main body, but inward in relation of the plug were smaller branches from which grew bundles of leaves, and the roots spiraled down past the camera's field of vision. And all of it was radiating outward from Shinji who was himself wrapped in branches of wood. But it did not appear to be in a constricted manner, more like the wood was trying to protect Shinji from the Angel's blast.

"What in the world?" Breathed Misato. "What is that Ritsuko?" She asked her college roommate and scientifically inclined friend.

"I don't know." Admitted the faux blonde.

"Ikari." Muttered Fuyutsuki.

"I know. This is not in the scenario."

"What do you think SEELE will say when they find out?"

"If they find out sensei. If. Until we understand how this happened, it will be for the best not to inform the old men. They tend to get worked up over the smallest of details that they cannot control or predict." Gendo paused as he adjusted his orange tinted glasses. "Should they find out about this before we can explain it then they will demand that the Third Child be turned over to them. And considering his performance just now it would not be in our best interest to lose him. So don't worry about the Committee, I'll deal with them."

* * *

Stepping off the elevator in her apartment building, Misato sighed at finally being home after such a long day. And what a day it had been.

The arrival of the Third Angel and the Third Child. Unit 01 activating without any power. And then the first battle between the Angels and the man made Evangelion.

But without a doubt the strangest thing was the Third Child himself. Shinji Ikari had nearly been squashed by the falling debris of a VTOL only to nimbly dodge with a series of acrobatics that she had only seen professionals accomplish. Then to repeat the action only this time weighted down by the weight of the First Child who, while no heavy weight, certainly weighed enough to burden anyone trying to jump, yet he did it seemingly effortlessly. Then there was the impossible miracle of Unit 01 activating without any power or even an entry plug, and as a response to Shinji's danger.

And who could forget the stunning performance he had put on when he finally got into the Eva. He was simply phenomenal, moving in a way that had taken Rei, the pilot who set the standard, and Asuka, a pilot considered a prodigy in comparison to Rei, months of training. And that was more than just talent. Misato was no expert but she knew from the way he controlled Unit 01 that Shinji had experience fighting.

Finally there was that swirling ball of energy, that 'Rasengan.' That tore its way through the Angel's AT Field, a supposed impossibility, and then damaged the Angel enough that it decided to commit suicide to destroy the Eva. And then there was all the plant life in the entry plug. Where had it come from, and why did it grow in the first place? Was it some sort of reaction to the Angel? And if so was it the Eva's reaction? The LCL's? Or perhaps was it Shinji himself that caused it?

Well she would probably know soon enough. After they managed to retrieve the Eva and unconscious Third Child, the boy was sent to the NERV medical where his condition would be carefully monitored until he was cleared to go. At the same time Ritsuko and the other techies would be running tests on the LCL, the plant life that had been carefully cut away from Shinji and the entry plug, and the Eva, as well as studying the data from the battle.

All of that had been hours ago in the dead of night and it was now minutes away from dawn, and after hours of paperwork that resulted from the battle all Misato wanted was a cold beer, hot bath, and a ready bed. She was so tired that she didn't even know that she was alone until she heard the "Good Morning."

Looking to her left she saw a man around her age with black eyes and light brown hair standing outside the apartment next to hers. His attire consisted of a simple blue shirt covered by a green vest, pants, and sandals. He also had some strange sort of head gear that was probably for some sport she wasn't familiar with. His arms were crossed, but he stance was relaxed and while his face was towards her his body was turned to the railing, clearly having been in the middle of stargazing or perhaps city watching before her arrival interrupted him. She surmised that he had only recently gotten back from the shelter and had decided not to sleep yet.

"Uh, yeah. Good morning." She eventually responded, her tone indicating that she would rather be saying good night. But that didn't stop this perky fellow.

"My names Yamato Tenzo and I just moved into this apartment. It's nice to be able to finally meet my neighbor." He greeted friendly, giving a small bow as is customary in Japan.

"Misato Katsuragi. Nice to meet you." She returned with another bow. "Listen it was nice meeting you, but I just got off from a rather long work shift and I really need to get some sleep."

"No problem, I just thought I would take the opportunity to introduce myself and set a good impression before my roommates get the chance to ruin it." Said Yamato jokingly as he turned around and opened his apartment door. "It was nice to meet you Captain Katsuragi, and I hope we get the chance to speak again soon."

Misato watched the new building tenet disappear behind his door before she her apartment and navigated through the filth the lined the floor. Deciding to forgo the bath she just grabbed a beer, gulped it down, and made sure Pen Pen had food before plopping down upon her futon, instantly falling asleep.

If she hadn't been so tired she might have realized that she never gave her rank to Yamato, and that he had the same leaf shaped symbol on his head gear as Shinji had on his headband.

* * *

**Author's Notes:** And so I finally bring out another chapter of Shinji Path of the Shinobi. I hope it is to everybody's liking. And sorry it took so long. At least I got this out just before finals here at my college.

I thought long and hard about giving Shinji a Kekkei Genkai and I originally was going to use the Sharingan, but then it was suggested to me by F-14 Tomcat Lover to use Mokuton. As I thought about it I figured that in the end Shinji could get more use from Mokuton then he could from Sharingan. That and it helped that we know so little about the fate of the Senju, compared to what we know of the Uchiha.

Now as I am sure you people have figured out I am a fan of Shinji/Rei pairings. Now this does not mean I hate Asuka. I do enjoy annoying her, and I am even a fan of a number of Shinji/Asuka pairing stories. I am just a bigger fan of Shinji/Rei (although I am also not adverse to Shinji being with both girls). So since you people knew that I am going to throw out this interesting tidbit. I plan for Misato to be paired with someone but not Kaji. And to add another tidbit that may or may not be related, I plan to bring more ninja over from the Hidden Continent. I am not going to say who or how many, but I will love to see peoples' guesses.

**Please Read and Review.**


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